Genetic diversity among plants sprouted from seven year old clones of mulberry (Morus indica var. S36) was studied using molecular markers such as ISSR and RAPD. The clones showed significant variability in sex expression and the sprouting behavior. These changes were appeared after seven years of rigorous pruning and training (pruned once in every 3-4months). Genetic diversity analysis revealed significant DNA polymorphism differences among these clones. Through multiple regression analysis, four DNA markers associated with specific traits were identified. Cloning, sequencing and bioinformatics analyses suggested probable involvement of transposable elements along with enzymes and transcriptional regulating factors. The results of this preliminary report call for detailed analyses at biochemical, physiological and molecular levels coupled with inheritance pattern of these markers and their corresponding phenotypic traits. The markers identified for sprouting and sex expression are of much use in early identification of hybrids with the respective traits.